The cool thing with MP3+ is a little switch which can be put into 'Digital only' mode. In this mode, the module doesn't touch the data, it only buffers it and output it on the TOSLink output.
I have a couple of DTS encoded wavefiles. I played one of them and my Onkyo decoded the DTS and I had a surround live performance with Eric Clapton in my speakers. Enough proof for me that the data is unaltered.